The purpose of the present study was to assess, in detail, the association between tooth agenesis (TA) and various sagittal skeletal malocclusion groups in a Japanese orthodontic population. One thousand and twenty patients were divided into skeletal Class I, II, or III malocclusion groups using the A point, nasion, and B point angle. TA was identified in each group using panoramic radiographs. Patients with class III malocclusion exhibited a significantly higher prevalence of third molar (M3) agenesis, bilateral and overall agenesis of the maxillary M3s than those patients with a class II malocclusion. Those with a Class II malocclusion demonstrated a significantly lower prevalence of overall agenesis of the mandibular M3s than those with class I or III malocclusions. There were no significant differences in the prevalence of agenesis of teeth other than the M3s between the skeletal malocclusion groups. In each group, there was significantly more M3 agenesis present in the maxilla than in the mandible, and agenesis of the incisors and second premolars was found more often in the mandible than in the maxilla. Sagittal jaw relationships were significantly associated with M3 agenesis but were not associated with agenesis of the maxillary and mandibular incisors and second premolars.